The evolutionary history and genetic composition of mammals has been strongly influenced by viruses. This is reflected by evolved mechanisms of host defense mediated by restriction factors that are in an arms race to win ...

Biofilm formation is a protective community building behavior in which microbes participate to respond to external stress or colonize new ecological niches. It is a primary mechanism used by pathogenic yeast to persist on ...

Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. One way in which cis-regulatory elements can be delineated is by their characteristic ...

A goal amongst modern biologists is to “compute” cellular and organismal function. This “computation” necessitates a holistic understanding of the biochemical mechanisms underlying different cellular states. Methods that ...

Massively parallel assays can dramatically advance our understanding of biological processes. Coupling them with modern mutagenesis techniques allows for fine mapping of the link between genotype and phenotype. In this ...

Massively parallel sequencing has accelerated the cataloging of cis-regulatory elements in mammalian genomes. However, it remains challenging to estimate the functional effects of variation in cis-regulatory elements. The ...

Biological systems have molecular mechanisms that allow them to maintain a constant phenotype despite environmental and genetic perturbations. These mechanisms can take the form of master regulator of robustness, gene ...

Though invisible to the naked eye, microbes are crucial to life as we know it. These tiny single-celled organisms are found in almost every known environment, helping to maintain balance across a vast array of ecological ...

Massively parallel technologies have dramatically reduced the cost and increased the throughput of DNA sequencing, transforming the study of patterns of genetic variation in human and model organisms, the genetic basis of ...

Translational control is an important mechanism of gene regulation, especially in gametogenesis and early embryogenesis, where there are periods of time in which there is no transcription. Previously transcribed mRNAs must ...

For my dissertation I focused on two distinct projects. In the first project, I analyzed early cancer exome datasets to identify patterns of mutation that offer insight into somatic mutational processes in humans. This ...

Somatic mutation plays a key role in the formation and progression of cancer. Differences in mutation patterns likely explain much of the heterogeneity seen in prognosis and treatment response among patients. Recent ...

The study of genomics is made possible by the creation of genome assemblies: strings of sequences that represent the DNA content of a species, or an individual within a species. However, genome assemblies do not spring ...

A central goal of biomedical research is to catalog genetic variation and uncover its causal relationship to phenotype. As humans are diploid organisms with two copies of each chromosome (except for the sex chromosomes in ...

Genome engineering tools and DNA sequencing technologies have improved dramatically over the past decade. These technologies are transforming many areas of research ranging from evolutionary biology to human disease. My ...

Accurately cross matching units of blood based on blood type is essential for successful transfusion therapy. ABO is the most clinically relevant blood group in transfusion therapy due to the presence of naturally occurring ...

The study of Mendelian disorders has been of immense utility in uncovering the genetic and molecular basis of numerous human traits, and has greatly furthered the identification of genes, the annotation of gene function ...

To survive in an ever-changing world, organisms need to rapidly adapt to new environments. In my dissertation, I address two molecular mechanisms that may contribute to rapid adaptation to new environments and help to ...

<italic>Cis</italic>-regulatory DNA encodes the circuitry that enables cell development and differentiation. <italic>Cis</italic>-regulatory DNA is densely populated by recogntition sequences for transcription factors and ...

Phenotypic variation among individuals within populations is ubiquitous in the natural world, and a preeminent challenge in biology is understanding the contribution of genetic variation to this phenotypic variation. Despite ...